Hi again guys.
So, I was wrong. I was told previously that the exhausts between 1199 and 1299 were not compatible, but after pressing the head project engineer further, they will physically fit fine.
To use a 1299 or SL exhaust on the 1199, you'll have to also use the vertical cylinder heat shield, the lower of the right fairing (it's got a different cutout for the larger diameter exhaust tube). There will also be minor issues with passenger pegs, and he said something about drilling a new hole/making a new mounting point on the subframe. Of course, then you'll also need a custom map as the SL one won't be good.
Sorry for my previous misleading info, hope that helps.